Biomechanics, Muscle Fibers, and How to Interface Experimental Apparatus to a Computer

132 Pages·2018·4.69 MB·English

by  Masataka Kawai (auth.)

Biomechanics, Muscle Fibers, and How to
Interface Experimental Apparatus to a Computer
Masataka Kawai
Biomechanics, Muscle
Fibers, and How to
Interface Experimental
Apparatus to a Computer
MasatakaKawai
DepartmentofAnatomyandCellBiology
TheUniversityofIowa
IowaCity,Iowa
USA
ISBN 978-3-319-72034-0 ISBN 978-3-319-72036-4 (eBook)
https://doi.org/10.1007/978-3-319-72036-4
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I could not tell how delighted and excited
I am about this new book by Masataka
Kawai! It is just what we have needed for
years, and it promises, at long last, to teach
the world about the complexities and
wonders of muscle — and how to deal with
it’s mechanical properties intelligently.
I also firmly believe that nobody is better
qualified to write on these topics and has
shown, through diligence and hard work,
the expertise that Kawai has. There is so
much to learn!
Marion J. Siegman, Ph.D.
Professor and Chair
Department of Molecular Physiology and
Biophysics
Thomas Jefferson University
Philadelphia, PA, U.S.A.
–
Preface About the Author and STEM
Disciplines
The subject that I have been practicing longest is electronics. I was 5 or 6 when
my father, Shunji Kawai , taught me how to make a radio. In those days,
theradioconsistedof4–5vacuumtubes(eachabout15cmtallwithoneusedasa
rectifier)withlitfilaments,andmanyadditionalparts.Radioswereveryexpensive
(costing 11,000 Yen or $30 then, which translates to $1,700 in today’s US cur-
rency) and my father could not afford one (his monthly pay as a school teacher
wasabout7,500Yen), sohewenttoNagoyaCity tolearnhow tobuildaradio. It
was fascinating to watch him make holes in an aluminum chassis with a hand-
powered drill, and attach parts with screws and nuts. He cut wires, put in insulat-
ing tubes, and soldered components together according to schematics. He taught
me how to perform all of these steps. Between us, we made ∼50 radios, and sold
them to villagers at a reduced price, which made us very popular. I did not know
how the radio works, but later made up my own theory because my science tea-
cher asked; subsequently, I confirmed my theory. In the meantime, my mother,
Yoshié , competed with my father as to what to teach me, and she taught me
how to knit. I ended up making a muffler and a sweater. Endless repetition of
(almost) thesamestepgavemepatienceandendurance whenIlaterwirednumer-
ousconnectionsincomputercircuits.
These experiences gave me a tremendous advantage over the years. The tall
vacuum tubes were gradually replaced with groove tubes (GT), miniature tubes,
transistors, low-cost integrated circuits (ICs), intermediate-level ICs (computer
chips),andlarge-scaleICs.Ateachstepinthisprogression,elementsbecamesmal-
ler, less expensive, and more reliable. At each stage, I had the opportunity to wire
them to make functional units. When I was a college junior, our math professor,
Akihiro Nozaki , taught us how to write a computer program using an
assembler language. The mainframe was a decimal-based computer that used a
rotating disk for its immediate memory and therefore was very slow, but I thought
itwascool.Ingraduateschool,mycolleagueRonTaylortaughtmehowtowrite a
Fortran program, with which I modified a primitive word processing program and
useditformyPhDthesiswithautomatedreferencing,figureandtablenumberings.
Mythesisadvisor,ProfessorErwin(Tack)Kuntz,encouragedmetouseoperational
vii
viii Preface–AbouttheAuthorandSTEMDisciplines
amplifiers, which are the basis of analog computers and essential for carrying out
biophysicalmeasurements(Sect.6.2.6).Duringmypostdoctoraltraining,mysenior
colleague, Professor Phil Brandt, obtained a 16-bit NOVA computer, and I was
able to interface my experiments (‘sinusoidal analysis’) to this computer. This
included D/A (digital-to-analog) conversion for experimental control, A/D conver-
sionfordataacquisition,aninterruptserviceprogram,programminginbothassem-
bler and compiler (Fortran) languages to control external devices and perform
experiments, and instant display of the results (Chap. 6). Luckily, the Fortran sys-
temhassurvived,andIstilluseprogramsIdevelopedmorethan40yearsago.
My fascination with biology started when I entered elementary school. I raised
silkworm larvae, fed them mulberry leaves, and watched them grow. They made
cocoons, metamorphosed to adult moths, mated, and laid eggs. I watched these
eggs hatch and grow into larvae again. I was certain by then that in life there are
twosexes,andthattheirgenesmustbemixedtoimprovegenes.Ialsocaughtbut-
terfly larvae, fed them until they formed cocoons, and watched them metamor-
phose into butterflies. This was more satisfactory than chasing butterflies and
catching them, because they escaped or got damaged when caught. When I was
14, my parents sent me to Tokyo to live with my aunt’s family and to attend mid-
dle and high schools there. Apparently, my parents felt that chasing butterfly lar-
vae was not an adequate education for me. In high school, my biology teacher,
Mr. Minoru Okuyama , taught us developmental biology, and it was
exciting to learn how an animal is formed starting from an egg. It was interesting
to know that development of the individual roughly recapitulates the evolution of
the species. Later in college, I took biochemistry, and was fascinated to see the
Watson and Crick DNA structure. My mentor, Professor Kazutomo Imahori
, said that it was the “Schrödinger equation” in biology. I rushed to
make a molecular model of DNA using wooden balls and sticks, encouraged by
ProfessorKoujiroIso .Thiswasoneofthose“wow!”moments.
Inthefirstyearofhighschool,Ibecameinterestedindifferentiationandintegra-
tion, and taught myself these subjects a couple of years ahead of the curriculum.
I derived the Taylor expansion series (Eq. 5.7), and a fundamental equivalence in
algebra (Euler’s formula): eiθ = cos θ + i sin θ (Eq. 5.6). Consequently, I was able
to follow the two-body problem in classical mechanics, and able to realize how a
planet moves around the sun (and wobbling of the sun), based on Newton’s law of
universal gravitation (force is inversely proportional to the square of the distance
between the two bodies) and acceleration (Eq. 1.7) by solving differential
equations set up based on these principles. My motivation came from a few hints
(dreams) our math teacher (Mr. Ichiro Takahashi ) and physics teacher
(Mr. Teizo Sasaki ) gave us during regular class hours, and from a
book of math formulas that my cousin, Mr. Toshisuke Kuniéda , had.
He was my roommate for about 12 months and taught me how to use the log table
for multiplication and power calculations. Consequently, I purchased a 7-digit log
table book, used an abacus to add (and multiply) the numbers, and calculated the
movements of planets. To get approximate answers, I used a slide rule. No hand-
heldcalculatorswereavailableinthosedays.
Preface–AbouttheAuthorandSTEMDisciplines ix
To open up a new field and perform new research, it is essential to develop a
newinstrument.WhenIenteredmyprofession,IwasluckythatIpossessedmany
of the skills needed. My strategy and principle in developing an instrument for
biological research is to let experimenters focus only on biology. While doing
experiments, one must not worry about electronics, mathematics, computer opera-
tions, or any other technical details. That is how I have been designing my auto-
matedexperimentalsystems.
Onethingmyfatherdidnotteachmewashowtomakemoney,althoughhehad
a keen interest in it and dreamed of receiving a million Yen from me as a gift; it
was unfortunate that this never happened. American children are generally better
off in this respect, because they learn this skill from an early age. However, many
sufferfrominadequatetrainingintheSTEM(science,technology,engineering,and
math) disciplines, which in the long run are more profitable than quick money-
makingmethods.Hopefully my bookwillstimulate theyoung generation to recog-
nize the importance of these disciplines. Although these may expose the human
racetoimmensedangerattimes,theywillsaveitfromextinctioninthelongrun.
***
Dr. Masataka Kawai (spelled in Japanese) is a native of Japan, and
received his B.A. from The University of Tokyo (Pure and Applied Sciences
),Ph.D.from Princeton University (Biology; Princeton,
NJ, USA), attended Physiology Course at Marine Biological Laboratory (Woods
Hole, MA, USA), and postdoctoral training at Columbia University (Muscle
biology; New York City, USA), where he became a junior faculty member. He is
now a professor of Anatomy and Cell Biology at The University of Iowa,College
of Medicine, Iowa City, IA, USA. He has taught histology to medical and dental
students for 35 years; he also taught principles of scholarly integrity to graduate
and postdoctoral students. He has recently learned gross anatomy and teaches this
subject. His hobbies include playing the piano, singing Japanese and Western
lyrics,gardening,skygazing,andtravels.
Symbols and Abbreviations Used
Symbols Definition
A Magnitude(amplitude)ofexponentialprocessA(Eqs.3.6,3.10)
A(t) Concentrationofcross-bridgesintheattachedstateA
A Steady-stateconcentrationofA
1
A Cross-sectionalarea(Fig.1.1)
C
A Totalconcentration(ofcross-bridges)(Eqs. 2.2,2.9)
T
ATPase TheATPhydrolysisrate(Eq.4.3)
ΔA Changeinhydrophobicsurfacearea(Eq.4.11)
HP
ΔA Changeinionicsurfacearea(Eq.4.12)
I
α≡2πa Apparent(observed)rateconstantofexponentialprocessA(Eq.3.6,
3.10,4.15,Fig.4.13)
α Rateconstantofdetachment(A→B),Schemes1,2(Figs.2.1,2.2)
α′ Rateconstantofattachment(B→A),Schemes1,2(Figs.2.1,2.2
B Magnitude(amplitude)ofexponentialprocessB(Eqs.3.6,3.10)
B(t) Concentrationofcross-bridgesinthedetachedstateB
B Steady-stateconcentrationofB
1
β≡2πb ApparentrateconstantofexponentialprocessB(Eqs.3.6,3.10,4.2)
β Rateconstantofattachment(B→C),Scheme2(Fig.2.2)
β′ Rateconstantofdetachment(C→B),Scheme2(Fig.2.2)
C Magnitude(amplitude)ofexponentialprocessC(Eqs.3.6,3.10)
C Capacitance(electricity,Sec6.1)
C(t) Concentrationofattachedcross-bridgesinC(Eq.2.12)
C Steady-stateconcentrationofC(Eq.2.12)
1
ΔC Heatcapacitychange(Eqs.4.8,4.9)
P
CPU Centralprocessingunit(Sect.6.4.1)
D MgADPconcentration(Eq.4.1)
ε Dielectricconstantofwater,ε =78.55at25°C(Eq.4.14)
r r
ε(t) Stepfunction(Sec.3.9,Table5.1)
F Force,Tension(Sect.1.1)
F(t) Forcetimecourse(Eq.3.10,Figs.3.1,4.9,4.14)
xi
xii SymbolsandAbbreviationsUsed
F Firstharmonicamplitudeofsinusoidalforceoscillation(Eqs.3.5,
1
5.39,5.40)
ΔG° Gibbsstandardfreeenergychange(Eq.4.7)
γ≡2πc ApparentrateconstantofexponentialprocessC(Eqs.3.6,3.10,4.1)
γ RateconstantofC→Atransition,Scheme2(Fig.2.2)
γ′ RateconstantofA→Ctransition,Scheme2(Fig.2.2)
η Viscousmodulus,viscosity(Eq.1.6)
ΔH° Helmholtz’sstandardfrpeeffiffiffiffieffiffinffiffiergy(enthalpy)change(Eqs.4.7,4.8)
i imaginarynumber,i= −1(Sect.5.2,Eq.5.1)
I Identitymatrix(math,Eq.5.47)
I Current(electricity,Eq.6.1)
Im Imaginarypart(ofacomplexnumber,Eq.5.1)
IS Ionicstrength(Eq.4.13)
K Matrixconsistingofrateconstants(Eq.2.29)
K AssociationconstantofMgADPtothemyosinhead(Eq.4.1,
0
Fig.4.7)
K AssociationconstantofMgATPtothemyosinhead(Eq.4.1,
1
Fig.4.7)
k Rateconstantofthecross-bridgedetachmentstep2(Eq.4.1,
2
Fig.4.7)
k−2 Reversalrateconstantofthestep2(Eq.4.1,Fig.4.7)
K2 Equilibriumconstantofthestep2,K2≡k2/k−2
k Rateconstantoftheforcegenerationstep4(Eq.4.2,Fig.4.7)
4
k−4 Reversalrateconstantofthestep4(Eq.4.2,Fig.4.7)
K4 Equilibriumconstantofthestep4,K4≡k4/k−4
K AssociationconstantofPitothemyosinhead(Eq.4.2,Fig.4.7)
5
k RateconstantoftheADPisomerizationstep6(Eq.4.3,Fig.4.7)
6
Kα EquilibriumconstantofA↔Btransition.Kα≡α/α′(Scheme2)
Kβ EquilibriumconstantofB↔Ctransition.Kβ≡β/β′(Scheme2)
L Length,strain(Sect.1.2)
L Amplitudeofsinusoidallengthoscillation(Eq.3.5)
1
L Sizeofsteplengthchange(Eqs.3.9,3.10)
1
l Debyelength(Eq.4.13)
D
λ Apparentrateconstant,λ≡α+α′(Eq.2.3,Scheme1)
λ ,λ Apparentrateconstants(Eqs.2.13,2.14,2.15)
2 3
Λ DiagonalmatrixconsistingofeigenvaluesofmatrixK(Eq.2.37)
m Mass(Eq.1.7)
ν Frequency(Eq.3.2)
ω Angularfrequency,ω=2πν,whereνisfrequency(Eq.3.2)
P Phosphateconcentration(Eq.4.2)
Pi Phosphate
2πa≡α RateconstantofprocessA(phase4)(Eqs.3.6,3.10)
2πb≡β RateconstantofprocessB(phase3)(Eqs.3.6,3.10)
2πc≡γ RateconstantofprocessC(phase2)(Eqs.3.6,3.10)
q AconstantneededtocalculateDebyelength(Eq.4.14)